Discovery of Covalent Inhibitors Targeting the Transcriptional Enhanced Associate Domain Central Pocket

Transcriptional enhanced associate domain (TEAD) transcription factors together with coactivators and corepressors modulate the expression of genes that regulate fundamental processes, such as organogenesis and cell growth, and elevated TEAD activity is associated with tumorigenesis. Hence, novel modulators of TEAD and methods for their identification are in high demand. We describe the development of a new “thiol conjugation assay” for identification of novel small molecules that bind to the TEAD central pocket. The assay monitors prevention of covalent binding of a fluorescence turn-on probe to a cysteine in the central pocket by small molecules. Screening of a collection of compounds revealed kojic acid analogues as TEAD inhibitors, which covalently target the cysteine in the central pocket, block the interaction with coactivator yes-associated protein with nanomolar apparent IC₅₀ values, and reduce TEAD target gene expression. This methodology promises to enable new medicinal chemistry programs aimed at the modulation of TEAD activity.

Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype

Targeted proteasomal and autophagic protein degradation, often employing bifunctional modalities, is a new paradigm for modulation of protein function. In an attempt to explore protein degradation by means of autophagy we combine arylidene-indolinones reported to bind the autophagy-related LC3B-protein and ligands of the PDEδ lipoprotein chaperone, the BRD2/3/4-bromodomain containing proteins and the BTK- and BLK kinases. Unexpectedly, the resulting bifunctional degraders do not induce protein degradation by means of macroautophagy, but instead direct their targets to the ubiquitin-proteasome system. Target and mechanism identification reveal that the arylidene-indolinones covalently bind DCAF11, a substrate receptor in the CUL4A/B-RBX1-DDB1-DCAF11 E3 ligase. The tempered α, β-unsaturated indolinone electrophiles define a drug-like DCAF11-ligand class that enables exploration of this E3 ligase in chemical biology and medicinal chemistry programs. The arylidene-indolinone scaffold frequently occurs in natural products which raises the question whether E3 ligand classes can be found more widely among natural products and related compounds.

Identification of a Novel Pseudo-Natural Product Type IV IDO1 Inhibitor Chemotype

Natural product (NP)-inspired design principles provide invaluable guidance for bioactive compound discovery. Pseudo-natural products (PNPs) are de novo combinations of NP fragments to target biologically relevant chemical space not covered by NPs. We describe the design and synthesis of apoxidoles, a novel pseudo-NP class, whereby indole- and tetrahydropyridine fragments are linked in monopodal connectivity not found in nature. Apoxidoles are efficiently accessible by an enantioselective [4+2] annulation reaction. Biological evaluation revealed that apoxidoles define a new potent type IV inhibitor chemotype of indoleamine 2,3-dioxygenase 1 (IDO1), a heme-containing enzyme considered a target for the treatment of neurodegeneration, autoimmunity and cancer. Apoxidoles target apo-IDO1, prevent heme binding and induce unique amino acid positioning as revealed by crystal structure analysis. Novel type IV apo-IDO1 inhibitors are in high demand, and apoxidoles may provide new opportunities for chemical biology and medicinal chemistry research.

The Highly Potent AhR Agonist Picoberin Modulates Hh-Dependent Osteoblast Differentiation

Identification and analysis of small molecule bioactivity in target-agnostic cellular assays and monitoring changes in phenotype followed by identification of the biological target are a powerful approach for the identification of novel bioactive chemical matter in particular when the monitored phenotype is disease-related and physiologically relevant. Profiling methods that enable the unbiased analysis of compound-perturbed states can suggest mechanisms of action or even targets for bioactive small molecules and may yield novel insights into biology. Here we report the enantioselective synthesis of natural-product-inspired 8-oxotetrahydroprotoberberines and the identification of Picoberin, a low picomolar inhibitor of Hedgehog (Hh)-induced osteoblast differentiation. Global transcriptome and proteome profiling revealed the aryl hydrocarbon receptor (AhR) as the molecular target of this compound and identified a cross talk between Hh and AhR signaling during osteoblast differentiation.

Cell-Based Identification of New IDO1 Modulator Chemotypes

The immunoregulatory enzyme indoleamine-2,3-dioxygenase (IDO1) strengthens cancer immune escape, and inhibition of IDO1 by means of new chemotypes and mechanisms of action is considered a promising opportunity for IDO1 inhibitor discovery. IDO1 is a cofactor-binding, redox-sensitive protein, which calls for monitoring of IDO1 activity in its native cellular environment. We developed a new, robust fluorescence-based assay amenable to high throughput, which detects kynurenine in cells. Screening of a ca. 150 000-member compound library discovered unprecedented, potent IDO1 modulators with different mechanisms of action, including direct IDO1 inhibitors, regulators of IDO1 expression, and inhibitors of heme synthesis. Three IDO1-modulator chemotypes were identified that bind to apo-IDO1 and compete with the heme cofactor. Our new cell-based technology opens up novel opportunities for medicinal chemistry programs in immuno-oncology.

The Pseudo-Natural Product Tafbromin Selectively Targets the TAF1 Bromodomain 2

Phenotypic assays detect small-molecule bioactivity at functionally relevant cellular sites, and inherently cover a variety of targets and mechanisms of action. They can uncover new small molecule-target pairs and may give rise to novel biological insights. By means of an osteoblast differentiation assay which employs a Hedgehog (Hh) signaling agonist as stimulus and which monitors an endogenous marker for osteoblasts, we identified a pyrrolo[3,4-g]quinoline (PQ) pseudo-natural product (PNP) class of osteogenesis inhibitors. The most potent PQ, termed Tafbromin, impairs canonical Hh signaling and modulates osteoblast differentiation through binding to the bromodomain 2 of the TATA-box binding protein-associated factor 1 (TAF1). Tafbromin is the most selective TAF1 bromodomain 2 ligand and promises to be an invaluable tool for the study of biological processes mediated by TAF1(2) bromodomains.

Identification of a Monovalent Pseudo-Natural Product Degrader Class Supercharging Degradation of IDO1 by its native E3 KLHDC3

Targeted protein degradation (TPD) modulates protein function beyond inhibition of enzyme activity or protein-protein interactions. Most degrader drugs function by directly mediating proximity between a neosubstrate and hijacked E3 ligase. Here, we identified pseudo-natural products derived from (-)-myrtanol, termed iDegs that inhibit and induce degradation of the immunomodulatory enzyme indoleamine-2,3-dioxygenase 1 (IDO1) by a distinct mechanism. iDegs boost IDO1 ubiquitination and degradation by the cullin-RING E3 ligase CRL2KLHDC3, which we identified to natively mediate ubiquitin-mediated degradation of IDO1. Therefore, iDegs increase IDO1 turnover using the native proteolytic pathway. In contrast to clinically explored IDO1 inhibitors, iDegs reduce formation of kynurenine by both inhibition and induced degradation of the enzyme and, thus, would also modulate non-enzymatic functions of IDO1. This unique mechanism of action may open up new therapeutic opportunities for the treatment of cancer beyond classical inhibition of IDO1.

THU0062 FUNCTIONAL MR IMAGING OF HUMAN MENISCUS IS ASSOCIATED WITH HISTOLOGICAL DEGENERATION

Background:

In OA, there is a close association of meniscus and cartilage pathologies. Meniscus degeneration and lesioning are critical risk factors for development of early OA. Hence, thisex-vivostudy assessed the responses to standardized loading of human meniscus samples as a function of degeneration and based on changes in their T1, T2 and T1ρ maps (as surrogate parameters of the tissue’s functionality).

Objectives:

Can meniscus functionality be visualized by serial quantitative MRI mapping technics?

Methods:

During total knee replacements, 45 meniscus samples of variable degeneration were harvested from the center of the lateral meniscus body (Fig. 1a1-a3). After preparation to standard, samples were subject to force-controlled loading using an MRI-compatible lever device that created compressive loading by torque ((Fig. 1a4-a5). For each sample and loading position, MRI measurements (as detailed below) were performed in the unloaded (δ0) and loaded configurations, i.e. loaded to 2 bar (δ1, 37.1 N compressive force, 0.67 Nm torque) and to 4 bar (δ2, 69.1 N, 1.24 Nm). Throughout all loading positions, morphological and quantitative imaging was performed using Proton Density-weighted and T1, T1ρ, and T2 mapping sequences (3.0 T, Achieva, Philips) based on standard turbospin-echo, inversion-recovery, spin-lock multi-gradient-echo, and multi-spin-echo sequences. For reference purposes, histological (i.e. Pauli classification) and biomechanical measures (i.e. Elastic Modulus) were obtained for each sample. Based on Pauli sum scores, samples were trichotomized as grossly intact, (n=14), mildly degenerated (n=16), and moderate-to-severely degenerated (n=15).

Figure 1.

Preparation of meniscus samples and details of the MRI-compatible loading device. The lateral meniscus (a1) was cut to standard size by use of a dedicated cutting block (a2) to eventually obtain lateral meniscus samples (from the body region) of standard dimensions (a3). These samples were then placed in a dedicated MRI-compatible loading device for pressure-controlled, quasi-static and torque-induced loading under simultaneous MR imaging (a4). Two parallel support beams allowed standardized positioning in the MRI scanner‘s bore (a5).

Results:

Morphologically, loading induced deformation and flattening in all samples (Fig. 2a). For T1, homogeneous loading-induced decreases in all samples were found, irrespective of degeneration (Fig. 2b). For T1ρ, increases in the apical zones of intact samples were observed, and decreases in degenerated samples (Fig. 2c). For T2, changes were ambiguous and incoherent (Fig. 2d).

Figure 2.

Serial morphological images and functional maps of histologically moderately degenerative human meniscus as a function of force-controlled loading. Serial PDw (a), T1 (b), T1ρ (c), and T2 maps (d) are displayed at increasing loading intensity (δ0: unloaded [a1-d1]; δ1: loaded to 2 bar [a2-d2]; δ2: loaded to 4 bar [a3-d3]). Histologically, this sample demonstrated signs of severe surface desintegration and disruption. Pauli sum score 12, i.e. moderate to severe degeneration (Pauli Grade III). In b – d, color-coded parameter value maps are overlaid onto the corresponding morphological images. Histological sections are stained with Hematoxylin-Eosin (e1) and Safranin O (e2).

Conclusion:

Meniscus functionality may be visualized using serial quantitative MRI mapping techniques. T1ρ may provide an imaging biomarker of relevant intra-tissue adaptations that seem to be associated with histological degeneration. The perspective evaluation of meniscus functionality may be indicative of incipient or manifest load transmission failure to the adjacent cartilage layer.

Disclosure of Interests:

Philipp Sewerin Grant/research support from: AbbVie Deutschland GmbH & Co. KG

Bristol-Myers Squibb Celgene GmbH

Lilly Deutschland GmbH

Novartis Pharma GmbH Pfizer Deutschland GmbH

Rheumazentrum Rhein-Ruhr, Consultant of: AMGEN GmbH AbbVie Deutschland GmbH & Co. KG Biogen GmbHBristol-Myers Squibb Celgene GmbH Chugai Pharma arketing Ltd. / Chugai Europe GmbHHexal Pharma Janssen-CilagGmbH Johnson & Johnson Deutschland GmbHLilly Deutschland GmbH / Lilly Europe / Lilly Global Novartis Pharma GmbH Pfizer Deutschland GmbH Roche Pharma Rheumazentrum Rhein-Ruhr Sanofi-Genzyme Deutschland GmbH Swedish Orphan Biovitrum GmbH UCB Pharma GmbH, Speakers bureau: AMGEN GmbH AbbVie Deutschland GmbH & Co. KG Biogen GmbHBristol-Myers Squibb Celgene GmbH Chugai Pharma arketing Ltd. / Chugai Europe GmbHHexal Pharma Janssen-CilagGmbH Johnson & Johnson Deutschland GmbHLilly Deutschland GmbH / Lilly Europe / Lilly Global Novartis Pharma GmbH Pfizer Deutschland GmbH Roche Pharma Rheumazentrum Rhein-Ruhr Sanofi-Genzyme Deutschland GmbH Swedish Orphan Biovitrum GmbH UCB Pharma GmbH, Lisa Dötsch: None declared, Daniel Truhm: None declared, Daniel Abrar: None declared, Sven Nebelung: None declared

Discovery of the sEH Inhibitor Epoxykynin as a Potent Kynurenine Pathway Modulator

Disease-related phenotypic assays enable unbiased discovery of novel bioactive small molecules and may provide novel insights into physiological systems and unprecedented molecular modes of action (MMOA). Herein, we report the identification and characterization of epoxykynin, a potent inhibitor of the soluble epoxide hydrolase (sEH). Epoxykynin was discovered by means of a cellular assay monitoring modulation of kynurenine (Kyn) levels in BxPC-3 cells upon stimulation with the cytokine interferon-γ (IFN-γ) and subsequent target identification employing affinity-based chemical proteomics. Increased Kyn levels are associated with immune suppression in the tumor microenvironment and, thus, the Kyn pathway and its key player indoleamine 2,3-dioxygenase 1 (IDO1) are appealing targets in immuno-oncology. However, targeting IDO1 directly has led to limited success in clinical investigations, demonstrating that alternative approaches to reduce Kyn levels are in high demand. We uncover a cross-talk between sEH and the Kyn pathway that may provide new opportunities to revert cancer-induced immune tolerance.